sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Å
NMR
1995-03-22
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.640 | 6.640 | 6.640 | 0.000 | 6.640 | 3 |
| Name: | Stromelysin-1 |
|---|---|
| ID: | MMP3_HUMAN |
| AC: | P08254 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.24.17 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.387 | 280.125 |
| % Hydrophobic | % Polar |
|---|---|
| 49.40 | 50.60 |
| According to VolSite | |
| HET Code: | INH |
|---|---|
| Formula: | C25H35N6O4 |
| Molecular weight: | 483.583 g/mol |
| DrugBank ID: | DB02747 |
| Buried Surface Area: | 46.12 % |
| Polar Surface area: | 178.58 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 6 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| -5.52174 | 1.21034 | 13.8239 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| N29 | O | ASN- 162 | 3.04 | 142.34 | H-Bond (Ligand Donor) |
| C1 | CG1 | VAL- 163 | 3.76 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 163 | 3.78 | 0 | Hydrophobic |
| O17 | N | LEU- 164 | 2.78 | 161.55 | H-Bond (Protein Donor) |
| C31 | CD2 | LEU- 164 | 3.54 | 0 | Hydrophobic |
| N6 | O | ALA- 165 | 2.6 | 125.34 | H-Bond (Ligand Donor) |
| C1 | CB | HIS- 166 | 4.4 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 197 | 3.26 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 198 | 4.24 | 0 | Hydrophobic |
| C8 | CB | HIS- 201 | 4.31 | 0 | Hydrophobic |
| C15 | CB | HIS- 201 | 3.72 | 0 | Hydrophobic |
| C12 | CB | LEU- 218 | 4.34 | 0 | Hydrophobic |
| C13 | CG | LEU- 218 | 4.07 | 0 | Hydrophobic |
| C34 | CB | TYR- 223 | 4.41 | 0 | Hydrophobic |
| C12 | CB | HIS- 224 | 4.49 | 0 | Hydrophobic |
| O4 | ZN | ZN- 257 | 2.05 | 0 | Metal Acceptor |
